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Microorganisms in Fish Feeds

Microorganisms in Fish Feeds, Technological Innovations, and Key Strategies for Sustainable Aquaculture

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Aquaculture feeds include fishmeal and fish oil, extracted from wildcaught fish such as sardines, and poses ecological, food security, and economic drawbacks. Here is a review on the recent development of using microorganisms, technological innovation, challenges, and opportunities to develop a low environmental footprint of aquaculture diet.

Aquaculture, the fastest growing food sector globally (8% average production increase/yr. for 1970–2014), now produces about half of all fish for human consumption, as global capture fisheries have reached or exceeded their sustainable limits and plateaued at~90 million tons/yr.

Aquaculture is the world’s most efficient protein generator and will play a key role in solving the grand challenge of feeding more than 9 billion people by 2050 by meeting the escalating demand for water, energy, and food while conserving environmental resources and protecting livelihoods.

Fed aquaculture grew 158% from 2000 to 2018 when it comprised nearly 60 million MT of production. The production of aquaculture feeds for the fed aquaculture is likewise expected to increase, and 73.15 million tons of feeds are projected to be used by 2025.


The environmental impacts and increasing price of aquaculture feed (aquafeeds) constrain U.S. aquaculture development. Feed has the largest overall environmental impact along the supply chain of intensive fed aquaculture, wherein the yields depend on giving animals nutritionally complete formulated feeds.

“The environmental sustainability of aquaculture food production systems is of critical concern due to its rapid expansion.”

Among the parameters that contribute to the overall environmental impacts, aquafeed was identified as an impact hotspot, and the production of feed ingredients contributed most to the global warming potential and other emissions.

Use of Fishmeal and Fish Oil in Aquafeed

Unfortunately, the fishmeal (FM) protein and fish oil (FO) ingredients in current commercial aquaculture feed (aquafeed) come from unsustainably sourced marine forage fish that are core components of marine food webs.

Currently, aquafeeds use more than 70% of the world’s fishmeal and fish oil, which are rendered from small wild-caught forage fish (such as herrings, sardines, and anchovies). Globally, approximately 16.9 million of the 29 million tons of ocean-caught small fish are currently used for aquaculture feeds each year.

“Even with the diminishing inclusion of fishmeal in aquaculture feeds, an estimated shortage ranging from 0.4 to 1.32 million metric tons of fishmeal could occur by 2050, significantly impairing the aquaculture industry growth.”

Analysts also projected that at the current rates of FM and FO consumption, aquaculture feed demands could outstrip the supply of forage fish by 2037, with disastrous consequences for the food security of billions of humans and for wild marine fish, mammals, and seabirds that forage on them.

Use of Terrestrial Crops and Oils in Aquafeeds and Environmental Challenges

Aquafeed manufacturers currently over-rely on terrestrial crops (e.g., soy, corn, canola) to replace fishmeal and fish oil; these would otherwise feed livestock or people. Industrial agriculture is facing a tremendous challenge due to agricultural pollution resulting in a loss of arable land.

“The increasing demand for these crops by aquaculture’s explosive growth could elevate the environmental problems that are caused by farming them, including high nutrient and chemical inputs, runoff that increases eutrophication, the clearing of sensitive lands (e.g., in Amazonia), high energy inputs, and greenhouse gas emissions.”

However, typically, the cultivation of terrestrial crops such as transgenic soy requires a large volume of water, pesticides, and fertilizers, and these also cause the deforestation of areas with high biological value.

Also, terrestrial plant protein and oil ingredients have several nutritional disadvantages such as a low nutrient digestibility due to high levels of antinutritional components, and a deficiency in limiting essential amino acids, for example, lysine, methionine, threonine, and tryptophan.


Replacing FM protein with terrestrial crop protein remains a significant challenge for the industry and has stimulated compensatory research such as adding single amino acids to provide missing essential amino acids.

In terms of the nutritional disadvantages of terrestrial crop oil, longchain polyunsaturated fatty acids (LCPUFA) such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are the major limiting fatty acids acid in terrestrial crop oils. These are the essential omega-3 fatty acids for salmonids, and the requirement is around 0.5–1.0% of the diet.

“The composition of omega-3 and other nutrients in farmed fish species has been altered, and this affects human nutrition, as there are decreases in the mineral concentration of iodine, selenium, vitamin D, and most significantly, omega-3 fatty acids in fish fillet.”

High percentages of vegetable oils in aquafeeds alter fish muscle fatty acid composition, notably reducing omega-3 such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), which aids with cardiovascular, cognitive, and neural development and provides other human health benefits.

Partially or totally replacing fish oil with crop oil also unfavorably changes the flesh fatty acid composition in many fish species. Over the past decade, the beneficial EPA and DHA content in farmed salmonids fillets has significantly declined, mainly due to the higher inclusion of vegetable oils in aquafeeds (Figure 1).

Microorganisms in Fish Feeds

Novel Aquafeed Ingredients

Microalgae Protein and Oil

The industrial-scale production of microalgae has gained momentum for their use in aquaculture feeds. Marine microalgae particularly have potential to replace fishmeal and fish oil in salmonids and other finfish feeds because of their high levels of fatty acid and protein content.

Marine microalgae, Nannochloropsis oculata, Isochrysis sp., and Schizochytrium sp. showed promise in aquafeed because they are rich in EPA, DHA, protein, key amino acids (methionine and lysine), lipids, and are good sources of minerals. A recent study showed that Isochrysis sp. is a highly digestible protein, amino acid, lipid, and fatty acids source for rainbow trout (Table 1).

Microorganisms in Fish Feeds

This species could be a good candidate for fishmeal and fish oil replacement in rainbow trout diets and can be used as a health-promoting omega-3, DHA supplement in diets.

A recent study showed promise in developing a fish-free feed for rainbow trout by combining marine microalgae Nannochloropsis sp., Isochrysis sp., and Schizochytrium sp.; the detected fillet DHA levels were similar (Figure 2).

Microorganisms in Fish Feeds

In addition, the cultivation conditions of microalgae, for example, light, temperature, and nutrient source, can also impact the phototrophically grown microalgal composition, including the fatty acid composition. It ultimately affects the consistent quality of the final product.

There has been extensive research on the capabilities of heterotrophic algae oils and their success in commercial trials. A number of aquafeed companies have recently begun commercially producing DHA-rich oil from Schizochytrium sp. for salmon feeds.

Yeast, Fungi, and Bacteria

Saccharomyces cerevisiae, various Aspergillus, and Fusarium venenatum are widely known, but other strains such as Candida utilis, Candida, Hansenula, Pichia, Torulopsis, and Kluyveromyces marxianus are also stimulating interest as protein ingredients for aquaculture feed.

Several yeast meals, for example, S. cerevisiae, Candida utilis, and K. marxianus have been used in salmon feeds. Candida utilis and K. marxianus are good sources of protein and could substitute up to 40% of the fishmeal without compromising growth. However, S. cerevisiae was reported as a poor protein ingredient for fish feed.

“Some bacterial strains can play an important role in producing very high crude protein contents (approximately 60 to 82% of dry cell weight) and essential amino acid levels, along with vitamins, phospholipids, and other functional compounds.”

There is great potential to produce bacterial protein, but more organisms need to be identified for commercial scale production. It is interesting to note that the bacteria can be cultured on agricultural wastes (rice straw, rice hulls, manure, and starchy residue), as the substrates attain a high level of protein.

Additionally, bacterial proteins contain other nutrients including lipids, vitamins, and minerals. Although bacterial proteins are very attractive for future aquafeed, the challenges associated with processing, the economy of scale, and their adoption globally need to be addressed.

Insect Meal

The aquafeed industry is actively seeking a diverse array of alternative feed ingredients for fishmeal, including insect meal. Insects could provide a sustainable source of protein for aquacultures using food waste.

As of now, the following species are the most studied for producing protein meals, and they account for the majority of the literature: black soldier fly, common housefly, yellow mealworm, lesser mealworm, house cricket, banded cricket, and field cricket.

Among these species, the black soldier fly (Hermetia illucens, L.; BSF) is considered the most attractive insect meal for aquafeed for salmonids, i.e., rainbow trout (Onchorhynchus mykiss) and Atlantic salmon (Salmo salar).

Several studies have shown promise with the use of insect meals in aquafeeds, and the inclusion of insect meals is still a recent development, with many uncertainties existing that could influence whether the aquafeed industry adopts insect meals on a large scale.

Fish Processing Byproduct

The processing of fish for human food generates byproducts such as heads, viscera, frames, skins, and others, such as tails, fins, scales, mince, blood, etc. These byproducts are actually good sources of protein and oil, from which fishmeal and fish oil can be yielded. Fish-processing byproducts are still not fully utilized. Approximately 25–35% of fishmeal comes from the byproducts of fish processing.

Approximately 10% of byproducts are generated by aquacultures, 19% of byproducts are generated by capture fisheries, and 71% of byproducts are generated by whole capture fisheries.

The largest volume of fish processing waste is produced in North America and Oceania. Fish wastes are mainly generated in the global south, mainly due to a lack of highquality ice, cold storages, and refrigerated transportation. Capturing fish processing byproducts is often not economically viable due to logistic and technical constraints.

Key Strategies to Measure Nutritional and Environmental Sustainability

Ingredients Digestibility

The digestibility of aquafeed ingredients is key information for formulating economically viable and environmentally responsible feeds, but limited digestibility data are publicly available for alternative ingredients. This lack of information often leads aquafeed manufacturers to extrapolate the nutritive value of ingredients from their chemical composition.

Because a simple biochemical analysis and the presence of protein and amino acids in the ingredients does not ensure the level of digestible proteins and amino acids required for particular fish species.

It is important to conduct digestibility experiments to identify the digestibility of ingredients and formulate the diet based on the digestible nutrient content, which can reduce feed costs, nutrient pollution (including phosphorus and nitrogen eutrophication emissions), and improve the feed conversion ratio of aquafeeds.

Feed Conversion Ratio (FCR)

The development of sustainable feed using alternative ingredients should be informed by the efficiency of feed with a lower FCR. A common measure of efficiency is the feed conversion ratio (FCR), calculated as the ratio of feed intake to weight gain.

It reflects the environmental performance of the aquaculture because it provides an indication of the phosphorus and nitrogen waste outputs in the aquatic environment with potential negative consequences of eutrophication, greenhouse gas emissions, loss of biodiversity, and other ecosystem services.

Additionally, the contribution of aquacultures to greenhouse gas emission is strongly related to the FCR and the origin of the feed components.

Now it is time to make more sustainable feed formulations for species such as carps, catfishes, tilapia, and marine shrimps. It is important to conduct more research on the LCAs of currently available unconventional feedstuff to better understand the more sustainable future ingredients for aquacultures.

Novel Technology for Improving

Ingredients Quality

Improving the overall feed efficiency/feed conversion ratio and digestibility of protein ingredients will help the aquafeed industry meet the global demand for these limited ingredients.

New technologies have been developing to process the ingredients that can improve the feed efficiency/feed conversion ratio, digestibility, and protein efficiency.

Extrusion Processing.

The novel extrusion technology offers the advantage of making use of a wider variety of ingredients. For example, twin screw extruder technology can be used to process, stabilize, and incorporate ingredients. The extruder has various capacities, along with drying, grinding, and other related equipment to conduct pilot-scale manufacturing tasks.

Use of Exogenous Enzymes in Aquafeed.

Protease enzymes may stimulate endogenous peptidases by improving protein digestibility and hydrolyzing proteinaceous antinutrients such as lectins, trypsin inhibitors, antigenic proteins, and antinutritional allergenic proteins such as glycinin, β-conglycinin, and kafrin.

High-quality proteases or cocktails can be developed for specific proteins (e.g., the keratin-rich poultry feathers) based on the digestive conditions (e.g., stomach or intestinal pH), which could help enhance dietary protein digestion and utilization.

Use of Additives in Aquafeed to Improve Palatability.

The supplementation of taurine with alternative ingredients would enhance the palatability of low fishmeal or fish-free feeds and improve digestion and lipid adsorption. Taurine is a neutral beta-amino acid derived from the metabolism of sulfur containing amino acids.

In the past, taurine was not considered an essential nutrient for fish, but recent research showed that it plays a key role in aquaculture nutrition to improve growth feed intake and feed utilization.

Challenges with Adopting and Opportunities to Adopt the New Aquafeeds

The aquafeed industry will use alternative ingredients only if it is at a cost competitive with soy and corn and at a constant quantity of supply.

Therefore, researchers and aquaculture industry stakeholders need a collaborative effort and need to pursue stepwise research to identify a prime alternative that will be productive and profitable while minimizing negative environmental, social, and economic impacts.

Towards this end, scientists should be pursuing stepwise research to find a sustainable solution, whether it is a novel ingredient or a combination of these ingredients or a coproduct or byproduct that can partially or fully replace crop proteins in aquafeeds, and to determine how this combination affects fish growth, flesh quality, and economic and environmental performances.


An evaluation of the sustainability of new ingredients is gaining attention. We should acknowledge that the major challenge is generating consistency with the supply of microalgal ingredients to produce large quantities on an industrial scale.

Another big challenge is the competitive price of unconventional ingredients with conventional ingredients. Price is the major constraint that will dictate the future course of the aquafeed sector and industry. Consequently, scaling up is a real block for these novel ingredients.

At this moment, adopting novel ingredients is still challenging and may not be equitable to all producers across the world. There are multiple regulatory, economic, and environmental challenges that accompany switching from conventional aquafeeds to ones based on innovative ingredients, especially for smaller producers and producers in developing countries.

Conclusions and Future Steps

Regarding progress towards the development of novel ingredients, it is imperative to determine the nutritional evaluations of each ingredient, which includes the determination of nutritional value, palatability and feed intake, and digestibility, and requires researchers to conduct nutritional feeding experiments in the lab and feeding/growth trials at commercial farms.

Some ingredients may require additional processing to improve digestibility, the FCR, and reduce the antinutritional factors. The various processing could also increase the opportunities to produce lower-cost protein-rich ingredients and might reduce the overall costs of production.

“In the final stage of the nutritional evaluation of alternative ingredients, a comprehensive economic analysis is also important to inform decisions about the inclusion of unconventional ingredients into diets that are cost competitive with coventional ingredients.”

To fully develop sustainable alternative ingredients, scholars must use systems-based approaches that integrate knowledge and expertise across multiple disciplines including fish nutritionists and aquaculture scientists to conduct on-farm feeding trials with farmers, environmental scientists, technoeconomic and lifecycle practitioners, extension scientists, and economists.

This is a summarized version developed by the editorial team of Aquaculture Magazine based on the review article titled “MICROORGANISMS IN FISH FEEDS, TECHNOLOGICAL INNOVATIONS, AND KEY STRATEGIES FOR SUSTAINABLE AQUACULTURE” developed by: PALLAB K. SARKER – Environmental Studies Department, University of California.
The original article was published on FEBRUARY, 2023 through Microorganisms.
The full version, including tables and figures, can be accessed online through this link: https://doi.org/10.3390/microorganisms11020439

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